rgexf: Build, Import and Export GEXF Graph Files

The first R package to work with GEXF graph files (used in Gephi and others). rgexf allows reading and writing graph files, including:

Nodes/edges attributes,
GEXF viz attributes (such as color, size, and position),
Network dynamics (for both edges and nodes, including spells) and
Edges weighting.

Users can build/handle graphs element-by-element or through data-frames, visualize the graph on a web browser through ~~sigmajs javascript~~ gexf-js library and interact with the igraph package.

Changes in rgexf version 0.16.3 (2024-06-27)

Dynamically loaded components in the Rd files were removed to comply with new CRAN policies.

Installation

To install the latest version of rgexf, you can use devtools

library(devtools)
install_github("gvegayon/rgexf")

The more stable (but old) version of rgexf can be found on CRAN too:

install.packages("rgexf")

Citation

citation(package="rgexf")

To cite rgexf in publications use the following paper:

  Vega Yon, G. G., (2021). Building, Importing, and Exporting GEXF
  Graph Files with rgexf. Journal of Open Source Software, 6(64), 3456,
  https://doi.org/10.21105/joss.03456

And the actual R package:

  Vega Yon G, Fábrega Lacoa J, Kunst J (2024). _netdiffuseR: Build,
  Import and Export GEXF Graph Files_. doi:10.5281/zenodo.5182708
  <https://doi.org/10.5281/zenodo.5182708>, R package version 0.17.0,
  <https://github.com/gvegayon/rgexf>.

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.

Examples

Example 1: Importing GEXF files

We can use the read.gexf function to read GEXF files into R:

# Loading the package
library(rgexf)

g <- system.file("gexf-graphs/lesmiserables.gexf", package="rgexf")
g <- read.gexf(g)
head(g) # Taking a look at the first handful

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.3" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd">
  <meta lastmodifieddate="2016-11-09">
    <creator>Gephi 0.9</creator>
    <description/>
  </meta>
  <graph defaultedgetype="undirected" mode="static">
    <attributes class="node" mode="static">
      <attribute id="modularity_class" title="Modularity Class" type="integer"/>
    </attributes>
    <nodes>
      <node id="11" label="Valjean">
        <attvalues>
          <attvalue for="modularity_class" value="1"/>
        </attvalues>
        <viz:size value="100.0"/>
        <viz:position x="-87.93029" y="6.8120565"/>
        <viz:color r="245" g="91" b="91"/>
      </node>
      <node id="48" label="Gavroche">
        <attvalues>
          <attvalue for="modularity_class" value="8"/>
        </attvalues>
        <viz:size value="61.600006"/>
        <viz:position x="387.89572" y="-110.462326"/>
        <viz:color r="91" g="245" b="91"/>
      </node>
      <node id="55" label="Marius">
        <attvalues>
          <attvalue for="modularity_class" value="6"/>
        </attvalues>
        <viz:size value="53.37143"/>
        <viz:position x="206.44687" y="13.805411"/>
        <viz:color r="194" g="91" b="245"/>
      </node>
      <node id="27" label="Javert">
        <attvalues>
          <attvalue for="modularity_class" value="7"/>
        </attvalues>
        <viz:size value="47.88571"/>
        <viz:position x="-81.46074" y="204.20204"/>
        <viz:color r="91" g="245" b="194"/>
      </node>
      <node id="25" label="Thenardier">
        <attvalues>
          <attvalue for="modularity_class" value="7"/>
        </attvalues>
        <viz:size value="45.142853"/>
        <viz:position x="82.80825" y="203.1144"/>
        <viz:color r="91" g="245" b="194"/>
      </node>
      <node id="23" label="Fantine">
        <attvalues>
          <attvalue for="modularity_class" value="2"/>
        </attvalues>
        <viz:size value="42.4"/>
        <viz:position x="-313.42786" y="289.44803"/>
        <viz:color r="91" g="194" b="245"/>
      </node>
            ...
     </nodes>
    <edges>
      <edge id="0" source="1" target="0"/>
      <edge id="1" source="2" target="0" weight="8.0"/>
      <edge id="2" source="3" target="0" weight="10.0"/>
      <edge id="3" source="3" target="2" weight="6.0"/>
      <edge id="4" source="4" target="0"/>
      <edge id="5" source="5" target="0"/>
            ...
     </edges>
  </graph>
</gexf>

Moreover, we can use the gexf.to.igraph() function to convert the gexf object into an igraph object:

library(igraph)

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

ig <- gexf.to.igraph(g)

op <- par(mai = rep(0, 4)) # Making room
plot(ig)

par(op)

Using the plot.gexf method–which uses the gexf-js JavaScript library–results in a Web visualization of the graph, like this:

plot(g)

A live version of the figure is available here.

Example 2: Static net

# Creating a group of individuals and their relations
people <- data.frame(matrix(c(1:4, 'juan', 'pedro', 'matthew', 'carlos'),ncol=2))
people

  X1      X2
1  1    juan
2  2   pedro
3  3 matthew
4  4  carlos

# Defining the relations structure
relations <- data.frame(matrix(c(1,4,1,2,1,3,2,3,3,4,4,2), ncol=2, byrow=T))
relations

# Getting things done
write.gexf(people, relations)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2024-06-30">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="static" defaultedgetype="undirected">
    <nodes>
      <node id="1" label="juan">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="79.2065507374859" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="91.9438021126364" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-79.815764224491" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="194.911331255884" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" weight="1"/>
      <edge id="1" source="1" target="2" weight="1"/>
      <edge id="2" source="1" target="3" weight="1"/>
      <edge id="3" source="2" target="3" weight="1"/>
      <edge id="4" source="3" target="4" weight="1"/>
      <edge id="5" source="4" target="2" weight="1"/>
    </edges>
  </graph>
</gexf>

Example 3: Dynamic net

# Defining the dynamic structure, note that there are some nodes that have NA at the end.
time<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time

     [,1] [,2]
[1,]   10   12
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA

# Getting things done
write.gexf(people, relations, nodeDynamic=time)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2024-06-30">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="dynamic" start="2" end="13" timeformat="double" defaultedgetype="undirected">
    <nodes>
      <node id="1" label="juan" start="10" end="12">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro" start="13" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew" start="2" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="23.8452238193327" y="113.652288092202" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos" start="2" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="77.7158886485609" y="-219.373757312507" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" weight="1"/>
      <edge id="1" source="1" target="2" weight="1"/>
      <edge id="2" source="1" target="3" weight="1"/>
      <edge id="3" source="2" target="3" weight="1"/>
      <edge id="4" source="3" target="4" weight="1"/>
      <edge id="5" source="4" target="2" weight="1"/>
    </edges>
  </graph>
</gexf>

Example 4: More complex… Dynamic graph with attributes both for nodes and edges

First, we define dynamics

time.nodes<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time.nodes

     [,1] [,2]
[1,]   10   12
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA

time.edges<-matrix(c(10.0,13.0,2.0,2.0,12.0,1,5,rep(NA,5)), nrow=6, ncol=2)
time.edges

     [,1] [,2]
[1,]   10    5
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA
[5,]   12   NA
[6,]    1   NA

Now we define the attribute values

# Defining a data frame of attributes for nodes and edges
node.att <- data.frame(letrafavorita=letters[1:4], numbers=1:4, stringsAsFactors=F)
node.att

  letrafavorita numbers
1             a       1
2             b       2
3             c       3
4             d       4

edge.att <- data.frame(letrafavorita=letters[1:6], numbers=1:6, stringsAsFactors=F)
edge.att

  letrafavorita numbers
1             a       1
2             b       2
3             c       3
4             d       4
5             e       5
6             f       6

# Getting the things done
write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges,
           edgesAtt=edge.att, nodeDynamic=time.nodes, nodesAtt=node.att)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2024-06-30">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="dynamic" start="1" end="13" timeformat="double" defaultedgetype="undirected">
    <attributes class="node" mode="static">
      <attribute id="att1" title="letrafavorita" type="string"/>
      <attribute id="att2" title="numbers" type="integer"/>
    </attributes>
    <attributes class="edge" mode="static">
      <attribute id="att1" title="letrafavorita" type="string"/>
      <attribute id="att2" title="numbers" type="integer"/>
    </attributes>
    <nodes>
      <node id="1" label="juan" start="10" end="12">
        <attvalues>
          <attvalue for="att1" value="a"/>
          <attvalue for="att2" value="1"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="116.263539042396" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro" start="13" end="13">
        <attvalues>
          <attvalue for="att1" value="b"/>
          <attvalue for="att2" value="2"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-162.569255531004" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew" start="2" end="13">
        <attvalues>
          <attvalue for="att1" value="c"/>
          <attvalue for="att2" value="3"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos" start="2" end="13">
        <attvalues>
          <attvalue for="att1" value="d"/>
          <attvalue for="att2" value="4"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="142.556872059596" y="89.0845907381178" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" start="10" end="5" weight="1">
        <attvalues>
          <attvalue for="att1" value="a"/>
          <attvalue for="att2" value="1"/>
        </attvalues>
      </edge>
      <edge id="1" source="1" target="2" start="13" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="b"/>
          <attvalue for="att2" value="2"/>
        </attvalues>
      </edge>
      <edge id="2" source="1" target="3" start="2" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="c"/>
          <attvalue for="att2" value="3"/>
        </attvalues>
      </edge>
      <edge id="3" source="2" target="3" start="2" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="d"/>
          <attvalue for="att2" value="4"/>
        </attvalues>
      </edge>
      <edge id="4" source="3" target="4" start="12" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="e"/>
          <attvalue for="att2" value="5"/>
        </attvalues>
      </edge>
      <edge id="5" source="4" target="2" start="1" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="f"/>
          <attvalue for="att2" value="6"/>
        </attvalues>
      </edge>
    </edges>
  </graph>
</gexf>

Code of Conduct

We welcome contributions to rgexf. Whether reporting a bug, starting a discussion by asking a question, or proposing/requesting a new feature, please go by creating a new issue here so that we can talk about it.

Please note that the rgexf project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms

Session info

devtools::session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       Ubuntu 22.04.4 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Denver
 date     2024-06-30
 pandoc   3.1.1 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version     date (UTC) lib source
 cachem        1.1.0       2024-05-16 [2] RSPM (R 4.4.0)
 cli           3.6.2       2023-12-11 [2] RSPM (R 4.3.0)
 devtools      2.4.5       2022-10-11 [2] RSPM (R 4.2.0)
 digest        0.6.35      2024-03-11 [2] RSPM (R 4.3.0)
 ellipsis      0.3.2       2021-04-29 [2] CRAN (R 4.1.1)
 evaluate      0.23        2023-11-01 [2] RSPM (R 4.3.0)
 fastmap       1.2.0       2024-05-15 [2] RSPM (R 4.4.0)
 fs            1.6.4       2024-04-25 [2] RSPM (R 4.3.0)
 glue          1.7.0       2024-01-09 [2] RSPM (R 4.3.0)
 htmltools     0.5.8.1     2024-04-04 [2] RSPM (R 4.3.0)
 htmlwidgets   1.6.4       2023-12-06 [2] RSPM (R 4.3.0)
 httpuv        1.6.15      2024-03-26 [2] RSPM (R 4.3.0)
 igraph      * 2.0.3       2024-03-13 [1] CRAN (R 4.4.0)
 jsonlite      1.8.8       2023-12-04 [2] RSPM (R 4.3.0)
 knitr         1.47        2024-05-29 [2] RSPM (R 4.4.0)
 later         1.3.2       2023-12-06 [2] RSPM (R 4.3.0)
 lifecycle     1.0.4       2023-11-07 [2] RSPM (R 4.3.0)
 magrittr      2.0.3       2022-03-30 [2] RSPM (R 4.2.0)
 memoise       2.0.1       2021-11-26 [2] RSPM (R 4.2.0)
 mime          0.12        2021-09-28 [2] RSPM (R 4.2.0)
 miniUI        0.1.1.1     2018-05-18 [2] CRAN (R 4.0.1)
 pkgbuild      1.4.4       2024-03-17 [2] RSPM (R 4.3.0)
 pkgconfig     2.0.3       2019-09-22 [2] CRAN (R 4.0.1)
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 profvis       0.3.8       2023-05-02 [2] RSPM (R 4.2.0)
 promises      1.3.0       2024-04-05 [2] RSPM (R 4.3.0)
 purrr         1.0.2       2023-08-10 [2] RSPM (R 4.2.0)
 R6            2.5.1       2021-08-19 [2] RSPM (R 4.2.0)
 Rcpp          1.0.12      2024-01-09 [2] RSPM (R 4.3.0)
 remotes       2.5.0       2024-03-17 [2] RSPM (R 4.3.0)
 rgexf       * 0.17.0      2024-06-27 [1] local
 rlang         1.1.3       2024-01-10 [2] RSPM (R 4.3.0)
 rmarkdown     2.27        2024-05-17 [2] RSPM (R 4.4.0)
 servr         0.30        2024-03-23 [2] RSPM (R 4.3.0)
 sessioninfo   1.2.2       2021-12-06 [2] RSPM (R 4.2.0)
 shiny         1.8.1.1     2024-04-02 [2] RSPM (R 4.3.0)
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 usethis       2.2.3       2024-02-19 [2] RSPM (R 4.3.0)
 vctrs         0.6.5       2023-12-01 [2] RSPM (R 4.3.0)
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 XML           3.99-0.16.1 2024-01-22 [2] RSPM (R 4.3.0)
 xtable        1.8-4       2019-04-21 [2] CRAN (R 4.0.1)
 yaml          2.3.8       2023-12-11 [2] RSPM (R 4.3.0)

 [1] /usr/local/lib/R/site-library
 [2] /usr/lib/R/site-library
 [3] /usr/lib/R/library

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